POP5

POP5 homolog, ribonuclease P/MRP subunit

Basic information

Region (hg38): 12:120578764-120581402

Links

ENSG00000167272 ∙ NCBI:51367 ∙ OMIM:609992 ∙ HGNC:17689 ∙ Uniprot:Q969H6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POP5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in POP5

This is a list of pathogenic ClinVar variants found in the POP5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-120579326-T-C		not specified	Uncertain significance (Jul 14, 2023)
12-120579394-T-C		not specified	Uncertain significance (Jan 15, 2025)
12-120579527-G-C		not specified	Uncertain significance (May 16, 2024)
12-120579549-T-C		not specified	Uncertain significance (Mar 03, 2025)
12-120579552-C-T		not specified	Uncertain significance (May 28, 2024)
12-120579563-C-G		not specified	Uncertain significance (Mar 08, 2025)
12-120579810-G-T		not specified	Uncertain significance (Feb 28, 2023)
12-120579876-T-C		not specified	Uncertain significance (Apr 04, 2023)
12-120581161-C-A		not specified	Uncertain significance (Jan 08, 2025)
12-120581169-T-C		not specified	Uncertain significance (Jul 10, 2024)
12-120581219-C-T		not specified	Uncertain significance (Mar 22, 2023)
12-120581345-G-C		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POP5	protein_coding	protein_coding	ENST00000357500	5	2635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.14e-7	0.218	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.527	78	92.3	0.845	0.00000438	1043
Missense in Polyphen		34	36.504	0.93141		406
Synonymous	0.692	31	36.3	0.854	0.00000161	313
Loss of Function	0.122	10	10.4	0.959	5.79e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP. {ECO:0000269|PubMed:11413139}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.419
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.346
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.786

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pop5

Gene ontology

• Biological process: tRNA 5'-leader removal;rRNA processing;tRNA processing;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: ribonuclease MRP complex;nucleoplasm;nucleolar ribonuclease P complex;multimeric ribonuclease P complex
• Molecular function: ribonuclease P activity;protein binding